Amplicon-based targeted sequencing of single circulating tumor cells
Whole-genome amplification of single circulating tumor cells introduces the coverage bias and false-positive errors that obscure their mutations, so this AMP 2019 poster enriches cancer-hotspot amplicons directly from cell lysate — no prior WGA — to read somatic variants one cell at a time.
Presented by RareCyte and the University of Washington.
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- Skipping whole-genome amplification recovered more of the true variants. In A549 model CTCs spiked into whole blood, 23 of 29 (79%) variants present in bulk genomic DNA were detected when the amplicon panel ran directly on cell lysate, versus 15 of 29 (52%) after WGA, and median read depth rose 48-fold over the WGA method.
- Direct sequencing cut the false-positive error rate 8-fold. The false-positive error frequency of the non-WGA single-cell libraries was 8-fold lower than the WGA libraries, consistent with amplification bias that appears as early as the pre-amplification step and increases throughout the WGA protocol.
- Known breast-cancer mutations were detected in individual patient CTCs. Across two metastatic breast cancer patients, oncogenic PIK3CA E542K appeared in 3 of 5 single CTCs from one patient and HER2-reactivating ERBB2 L755S in 3 of 5 CTCs from the other; each variant was also present in that patient’s cell-free DNA, while the matched white blood cells read 0%.
